A Shift in <i>Begomovirus coheni</i> Populations Associated With Tomato Yellow Leaf Curl Disease Infecting Tomato Cultivars in the Southeastern United States

ABSTRACT Tomato yellow leaf curl virus (TYLCV) is a major pathogen causing tomato yellow leaf curl disease (TYLCD), significantly impacting tomato production. Full‐length genome sequences of three TYLCV isolates were generated from commercially grown tomato cultivars in Georgia, USA. Nucleotide sequence identity confirmed the presence of TYLCV ( Begomovirus coheni ). A genome map illustrating all open reading frames and their coordinates in conjugation with the guanine‐cytosine (GC) dinucleotide distribution was mapped. Sequence analysis gave a phylogenetic dendrogram forming a clade consisting of TYLCV isolates reported from European and Mediterranean countries. Analysis of TYLCV isolates infecting tomatoes in the United States revealed the formation of at least two distinct clades based on the year of occurrence. Agrobacterium ‐mediated inoculation of a clone with partial tandem repeats of the TYLCV‐Georgia (TYLCV‐GA) isolate caused severe symptoms on tomato cultivars 30 days post‐inoculation. The infectious clones were acquired by whiteflies and transmitted to tomato cultivars, expressing severe symptoms and confirming its pathogenicity in natural host plants. Genetic variability parameters of the TYLCV population, including three full‐length TYLCV‐GA, showed purifying selection or recent population expansion of tomato‐associated TYLCV isolates/variants in the United States. Synonymous and non‐synonymous mutations corresponding to the Geminivirus Rep Sequence (GRS) motif, motif III of the Rep protein, and WCCH motif of the coat protein indicated genetic mutations in the conserved motifs. Our study demonstrated that TYLCV‐GA is widespread on a commercial farm scale in Georgia and causes severe disease in tomato cultivars. A population shift in begomoviruses associated with TYLCD could facilitate the emergence of TYLCV‐GA in natural conditions.